targetHub API Documentation
targetHub is a database of miRNA-mRNA interactions. The interaction data is obtained various external data sources and in some cases computed in-house by algorithms implemented for miRNA target prediction.
The target prediction methods/data sources used to populate targetHub are shown in the following list. You can refer the documentation section for more details
Other sources may be incorporated in the future. These sources of information have been combined into a simple CouchDB database. As a consequence, we can build tools that make it possible to find the miRNA-gene interactions from various types of identifiers by different criteria using the CouchDB views.Input and Output
All calls to read data or query results from the targetHub web service are made using RESTful HTTP calls. All results are returned in JavaScript Object Notation (JSON).targetHub follows the usual CouchDB conventions. Each object has a unique identifier, which in this case is given by pair of miRNA and a protein-coding gene seperated by a colon [depicting their interaction].
For example, the identifier of the document depicting the interaction of mir-212 with BRCA1 gene (Entrez Gene: 672) would be "hsa-mir-212:672". To get the JSON representation of this CouchDB document, send a HTTP GET request to the following URL:
HOSTNAME/tarhub/hsa-mir-212:672
Views
CouchDB queries are also known as views. The available views define the main API. In the current version, all views used to query the database are contained in the "basic" design document. You can get a copy of the design document by sending an HTTP GET request to the URL:
HOSTNAME/tarhub/_design/basic
Views are defined in targetHub to enable the user to query database by two different search options using three types of identifiers.
Search Options
- Evidence Count
- Specific Methods Note:When querying targetHub by specific methods, the methods should be specified in alphabetical order seperated by the sign "+"
- [ By Gene] Entrez Gene identifier
- [ By stem-loop miRNA] miRBase identifier
- [ By mature miRNA] miRBase mature miRNA identifier
HOSTNAME/tarhub/_design/basic/_view/
- The specification for URLs limits the use of allowed characters to only a limited subset of the ASCII character set. The "+" sign in the JSON query need to be encoded to the corresponding code (%2B) to specify a query.
- The option include_docs can be used [include_docs=true], to automatically fetch and include the document which emitted each view entry of the database for a particular query.
Query by gene [Entrez Gene ID]
| HTTP Call | Search By | Result |
|---|---|---|
| by_geneIDcount?key=["672",3] | Evidence Count | miRNA-target interactions of Entrez Gene "672" (BRCA1) that are supported by exactly three data sources/methods |
| by_geneIDcount?startkey=["672",3]&endkey=["672",{}] | Evidence Count | miRNA-target interactions of Entrez Gene "672" (BRCA1) that are supported by atleast three data sources/methods |
| by_geneIDmethod?key=["672","mirtarbase"] | Specific Method | miRNA-target interactions of Entrez Gene "672" (BRCA1) that are supported by miRTarBase |
| by_geneIDmethod?key=["672","miranda+pictar4+targetscan"] | Specific Method | miRNA-target interactions of Entrez Gene "672" (BRCA1) that are supported by three methods miRanda, PicTar (4)and TargetScan |
geneSmash: Web-service for gene ID conversion
geneSmash is a a gene-centric couchDB database containing information about human genes from various sources. The gene-based search interface for the targetHub website is built using geneSmash. The geneSmash web service converts any of the input gene identifier types to Entrez Gene. The Entrez Gene identifiers can then be passed on to query targetHub to retreive the relevant miRNA-target interactions. Similarly, when using the targetHub API you can utlize the geneSmash API to convert your gene identifier to Entrez Gene before querying targetHub [Sample Code in R]. Check geneSmash documentation for detailed information on web-service for gene ID conversion.
Query by stem-loop miRNA [mirbase ID]
| HTTP Call | Search By | Result |
|---|---|---|
| by_miRNAIDcount?key=["hsa-mir-212",4] | Evidence Count | miRNA-target interactions of miRNA "hsa-mir-212" that are supported by exactly four data sources/methods |
| by_miRNAIDcount?startkey=["hsa-mir-212",3]&endkey=["hsa-mir-212",{}] | Evidence Count | miRNA-target interactions of miRNA "hsa-mir-212" that are supported by atleast three data sources/methods |
| by_miRNAIDmethod?key=["hsa-mir-212","pictar5"] | Specific Method | miRNA-target interactions of miRNA "hsa-mir-212" that are supported by PicTar (5) |
| by_miRNAIDmethod?key=["hsa-mir-212","miranda+mirtarbase+pictar4+targetscan"] | Specific Method | miRNA-target interactions of miRNA "hsa-mir-212" that are supported by four methods miRanda, miRTarBase, PicTar (4)and TargetScan |
Query by mature miRNA [mirbase]
| HTTP Call | Search By | Result |
|---|---|---|
| by_matureMIRcount?key=["hsa-miR-212-3p",4] | Evidence Count | miRNA-target interactions of mature miRNA "hsa-miR-212-3p" (stem-loop: hsa-mir-212) that are supported by exactly four data sources/methods |
| by_matureMIRcount?startkey=["hsa-miR-212-3p",4]&endkey=["hsa-miR-212-3p",{}] | Evidence Count | miRNA-target interactions of mature miRNA "hsa-miR-212-3p" (stem-loop: hsa-mir-212) that are supported by atleast four data sources/methods |
| by_matureMIRmethod?key=["hsa-miR-212-3p","targetscan"] | Specific Method | miRNA-target interactions of mature miRNA "hsa-miR-212-3p" (stem-loop: hsa-mir-212) that are supported by TargetScan |
| by_matureMIRmethod?key=["hsa-miR-212-3p","miranda+targetscan"] | Specific Method | miRNA-target interactions of mature miRNA "hsa-miR-212-3p" (stem-loop: hsa-mir-212) that are supported by two methods miRanda and TargetScan |
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